| Comparing Structure Files [message #1470] |
Wed, 12 January 2022 13:42  |
biolive31!!
Messages: 5
Registered: January 2022
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Junior Member |
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Good morning I'am Olivier a new datawarior user !
I tried to use the "Find similar compound in other file" tool but it doesnt work.
I know that some molecule are similar to those in the "other file " and the tool did not find it . Any molecule is find similar. I try both comparison method , even to 70% of similarity any similar molecule is find .
Could you help me ?
Thank you
Olivier
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| Re: Comparing Structure Files [message #1471 is a reply to message #1470] |
Thu, 13 January 2022 23:44  |
nbehrnd
Messages: 224
Registered: June 2019
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Senior Member |
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Dear Oliver,
your question contains little material to replicate your finding. Thus, it is difficult to identify a plausible cause for your observation.
On the other hand, I created two tiny libraries of drug-like molecules (chemistry -> generate random molecules) where the defaults were modified slightly (instead of 1000, I opted for 100 molecules each). Subsequently, while reading set_b.dwar, I selected set_a.dwar for a comparison. With a structureFp threshold lowered to 70%, DW identified 13 molecules as similar enough. Raw data, set up of the parameters, and result files in the attachement below. Perhaps the threshold set by you was too high? The criterion «structure exact» isn't a restraint, it is meant as a constraint*); any variation in the molecule to check vs. the reference molecule and the test assigns the two as dissimilar.
*) which may be weakened in regard of stereochemistry, tautomers, or application on the largest fragment only.
Norwid
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| Re: Comparing Structure Files [message #1580 is a reply to message #1539] |
Tue, 05 April 2022 16:47 |
thomas
Messages: 715
Registered: June 2014
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Senior Member |
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Dear Olivier and Norvid,
I am sorry that it took such a long time for me to realize the issue here. When comparing an open window against an SD-file and if columns shall be copied from the SD-file into the open window, then DataWarrior used to parse the SD-file to the end in order to create a list of existing columns. When then starting comparing molecules, it didn't find any molecules, because it was already at the end of the SD-file and, therefore, it never found matching molecules in this case. This should now be fixed in the current dev version.
Thomas
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